What is CytoGEDEVO?

CytoGEDEVO is a Cytoscape plugin that implements the GEDEVO method for pairwise global network alignment. This is a new version that obsoletes the old version published in 2013.

Free download is available from the Cytoscape app store and the download section below.

GEDEVO stands for Graph Edit Distance + EVOlution and it utilizes the evolutionary computing strategies for solving the so-called network alignment problem using Graph Edit Distance.

Optionally, any number of other node similarity or distance measures can be incorporated to guide the alignment process. CytoGEDEVO can align networks with focus on biological data, given that such are provided, and is even able to ignore network topology completely if desired (note that while the name might suggest otherwise, this new version of GEDEVO is not limited to the GED!).

What is Network Alignment?

Network Alignment is a computationally hard bioinformatic problem. It aims to find the "best" one-to-one correspondence between nodes from two input networks with or without using external knowledge, such as sequence similarity.

Network Alignment, applied to Protein-Protein Interaction (PPI) networks, finds its applications in the validation of interactions and the prediction of new ones, as well as for extracting conserved subnetworks in a set of given PPI networks. Network Alignment is a novel basis, in addition to sequence alignment (DNA and amino acids), for further interspecies network analysis in drug development, including (functional) knowledge transfer between species.

Illustration of GED

Transforming graph G1 graph into G2

Cost of edit operations:

GED(G1, G2) = 6

Downloads

Cytoscape app/plugin

We recommend to install CytoGEDEVO from within Cytoscape using its app manager. Alternatively, download the JAR file from the Cytoscape App store.

Commandline versions

Additional files

Source code

Further information

Bug tracker

If you encounter any issues or bugs, please report them so that they can get fixed.

Citation

Malek M, Ibragimov R, Albrecht M, Baumbach J (2015) CytoGEDEVO - Global alignment of biological networks with Cytoscape. Bioinformatics. 2015 (in press).

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